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The Enterprise is ordered to evacuate a research station on the planetMinara II whose sun, Minara, is about to go nova. Kirk, Spock, and McCoybeam down to the planet, but find the six-month old research station abandoned. Informed of an imminent solar flare with high levels of cosmic rays, Kirk orders Scotty to take the Enterprise out of orbit, reasoning that the landing party will be protected by the planet's atmosphere during the 74.1 solar hours it will take for the flare to subside. Upon consulting a visual tape recording, the landing party discovers that the two researchers, Drs.Ozaba and Linke, had mysteriously disappeared three months earlier amid a flurry of seismic activity and deafening noise. Soon after this discovery the landing party similarly vanishes.

Moments later Kirk, Spock, and McCoy find themselves 121.32 meters below the planet's surface, transported by a matter-energy scrambler similar to their transporter technology. After wandering through a cavern, they encounter a humanoid woman reclining on a dimly lit, cross-shaped couch. McCoy wants to go forward because she looks harmless, but Spock reminds him that the sand bats of Manark IV look like inanimate rock crystals until they attack.

The woman awakens but does not respond to Kirk's questions. McCoy determines that she does not have any vocal cords, not even vestigial, indicating that she comes from a species of mutes. Kirk observes that she is like the naturally mute people of the civilization on Gamma Vertis IV. McCoy names her Gem.

Two different-looking humanoid aliens suddenly appear to the landing party. Identifying themselves as Vians, Thann and Lal, they make it clear that they know the identities of the landing party. They demand that Kirk not interfere, and when he approaches they stun him with a hand-held control device with a red button on the face. Kirk points out that if the Vians know who they are, they also must know that they come in peace and that their prime directive prohibits interference.

The Vians momentarily trap the landing party in a force field while they tend to Gem. McCoy tells Kirk not to fight the force field since it interferes with the body's metabolism. The Vians correct McCoy's hypothesis, saying that the field draws its strength from their bodies' energy and the more they resist the stronger the field becomes. They depart and the field vanishes.

Kirk has suffered a cut on his forehead and when he touches Gem to see if she is all right, she recoils in pain. Gem composes herself and then touches Kirk's wound. With a flash, the wound is transferred to Gem's forehead. A doubting Kirk touches her wound and notes the blood on his finger. Suddenly, the wound on Gem's forehead quickly heals as well. McCoy, observing, is clearly impressed by her ability to heal and surmises that Gem is an empath. Her emotional system is so sensitive that it feels the pain of another and that pain becomes part of her, before she dissipates it.

Spock finds that his tricorder now gives readings of electronically sophisticated devices. They find a laboratory with the deceased Drs. Linke and Ozaba trapped in clear tubes marked with their names, their bodies twisted in agony.

There are also tubes designated for McCoy, Kirk, and Spock. One of the Vians appears and says there is need for more testing. He blames the weakness of their bodies. While Kirk talks, Spock sneaks up behind and gives the Vian a Vulcan nerve pinch. As the landing party walks off toward a passage to the surface Spock has located, the Vian arises. Apparently the nerve pinch was less effective than normal. He joins his companion, and they share a look that indicates they are impressed with the crew.

At the surface, Kirk tries to contact the Enterprise with his communicator but the ship is out of range. He leads the landing party through a storm back to the research station, where it appears to them that Scotty and two redshirts are waiting for them. Spock and McCoy go ahead with Gem, but Kirk spots the Vians watching them and stops. He moves toward them, but one uses his weapon to make Kirk move in slow motion. He remarks, "Their will to survive is great. They love life greatly to struggle so. The prime ingredient."

When Spock and the others reach the research station, the images of Scotty and the redshirts suddenly vanish. Gem brings Spock and McCoy back to where Kirk is confronting the Vians. They announce that they only need one specimen, so Kirk sends the others back to the ship. The Vians transport them away, and then recapture Kirk.

The Vians bring Kirk back to the laboratory. Here, where the bodies of Ozaba and Linke are displayed like specimens, the Vians chain a shirtless Kirk by his arms to the ceiling. They tell him they want to witness his courage and will to survive. Using their hand devices, they torture Kirk.

Spock and McCoy have been transported to the chamber where they originally met Gem. When Kirk and Gem are also transported there, Spock and McCoy are trapped in a force field. With McCoy's encouragement, Gem heals Kirk's wrist wounds. When she finishes, she collapses. The process is physically draining and, apparently, has its limits.

The Vians return and indicate that for their next experimental subject Kirk must choose either Spock or McCoy To make the decision all the more difficult, the Vians indicate that there is a 93% chance that Spock will suffer brain damage and permanent insanity, and an 87% chance that McCoy will die.

Spock analyzes the confiscated Vian hand device. McCoy, uncomfortable with the wait, comments that it's not natural for a Human to live underground. Spock points out that some Humans spend the majority of their lives "beneath the surface." McCoy responds, "I'm a doctor, not a coal miner." Spock tells McCoy that he is recording his notes of the hand device in the tricorder in the event that he is taken by the Vians so that McCoy and Kirk can continue his work and escape.

Plagued with symptoms resembling the bends, Kirk is caught off guard by McCoy, who renders Kirk unconscious with a hypospray. Now in command, Spock declares that he will go with the Vians at the appointed time, but McCoy sneaks behind Spock and renders him unconscious as well, intending to sacrifice himself for his two friends. All of these noble efforts at self-sacrifice are observed by Gem.

Taken to the Vians' laboratory, McCoy undergoes extensive torture. Meanwhile, now awake, Spock has come to understand the Vian hand-held devices. They are control units, not control mechanisms – they are not a mechanical device at all. They are tuned to the pattern of electrical energy of the person who uses it and are activated simply by mental commands. Being most familiar with his own brain pattern, Spock retunes the device to his own pattern. Kirk points out that it is strange that the Vians let them keep the device if they would be able to understand it. They must want Spock and Kirk to escape and to leave McCoy behind.

Spock completes the modifications and says he may only be able to effect one transport. He suggests there is enough energy to go back to the Enterprise, but Kirk would prefer to go to McCoy, stating "the best defense is a strong offense - and I intend to start offending right now." Spock transports Kirk, Gem and himself to the laboratory, where they find McCoy on the verge of death and the Vians nowhere to be found.

Spock and Kirk release McCoy from his chains. He is in bad shape; with barely a pulse, he has severe heart damage, congestion in both lungs, and his circulatory system is in danger of collapse. He is bleeding into the chest, his spleen and liver are hemorrhaging and his kidneys have 70% failure. Spock informs Jim that McCoy is dying and the best he can do is make him comfortable. McCoy compliments Spock on his bedside manner.

McCoy tortured by Vians

Kirk suggests that Gem could heal McCoy, but he is not sure if the attempt will kill her. At least, he hopes, she can improve his condition so that he can be healed on the Enterprise. Suddenly the Vians appear and trap Spock and Kirk in a force field; they demand that the Humans not interfere and allow Gem to make her own choice without urging or forcing. It is their wish to see if Gem will attempt to help McCoy on her own at the cost of her own life – the completion of their test.

At this time they explain to Kirk, Spock, and the dying McCoy that they have been part of an experiment. They have the power to save only one species from the impending nova, and so they wished to test whether Gem's species is worthy of being saved. Apparently the Vians want to be certain that she has learned the principles of self-sacrifice, the will to survive, the passion to know and the love of life from her contact with the humans. These qualities, they say, make a civilization worthy to survive.

As they speak, Gem has approached McCoy. The Vians are pleased that compassion has entered her "life-system." She moves her hands on McCoy's face, transferring his injuries to her. McCoy awakes, but Gem collapses, sobbing. She tries to help him more, but moves away in fear.

Inside the force field, Spock points out that Gem is not the only one who can save McCoy: of course, the Vians must have the power to help. The Vians respond that McCoy's life is not important, but what is important is their experiment.

McCoy starts coughing and Gem returns to his side. McCoy asks that Gem not touch him. If she touches him, she will die, and he cannot take life – even to save his own.

Spock realizes that if he and Kirk were to suppress their emotion, they would be able to escape from the force field. Spock escapes first and takes the other control device from the Vians. Kirk demands that the Vians save McCoy but they refuse, demanding that the experiment continue. Offering to give her life, they say, is not sufficient. She must sacrifice her life.

Kirk gives the Vians their control devices and reprimands them. They have forgotten what it means to feel the emotions they want Gem to experience. He scorns their lack of love and compassion, saying that they are nothing but intellect. The Vians heal McCoy and, taking Gem with them, teleport from the laboratory, presumably to save Gem's species. The landing party returns safely to the Enterprise, which has returned to orbit after the solar flare has subsided.

Back on board, Kirk says he is awed by the element of chance that brought them into contact with Gem. Scotty observes that she must have been like the 'pearl of great price' (Matthew 13:45-46 of the Humans' Christian Bible). McCoy is pleased that, in the end, it was the strength of Human emotion that overcome their captivity by the dispassionate, intellectual Vians.

"Captain's log, stardate 5121.5. Orbiting the second planet in the Minarian star system. This star has long given evidence of entering a nova phase and six months ago, a research station was established to make close-up studies of the star as its end approaches. Minara is now entering a critical period, and the Enterprise has been ordered to evacuate the station before the planet becomes uninhabitable. Yet our attempts to contact the station's personnel have been, so far, unsuccessful."

This was one of the few episodes to quote the Bible, specifically Psalm 95, verse 4: "In His hands are the deep places of the Earth. The heights of the mountains are His also", and the Gospel of Matthew, 13:45-46: "Again, the kingdom of heaven is like unto a merchant man, seeking goodly pearls: who, when he had found one pearl of great price, went and sold all that he had, and bought it."

"The Empath" has similarities to a 1963 Outer Limits segment called "Nightmare". In that episode, Humans are brutally interrogated by aliens in a minimalistic set. John Erman also directed "Nightmare", Willard Sage (Thann) was one of those behind the interrogations, and Robert Justman was, at that time, an assistant director on the series. (The Star Trek Compendium)

Though identified as Thann and Lal in the closing credits, the two Vians are never called by their proper names on-screen.

The tripodal device in the center of the Vian laboratory also appeared first in the episode "Spock's Brain" as the framework connected to the black box (by "light rays") that housed Spock's brain. It is inverted here from its position in that episode.

The orange-red flickers that accompany the Vian transporter effect are frames of the same effect created to represent the MedusanambassadorKollos.

After Dr. McCoy is tortured by the Vians, the distressed tunic that DeForest Kelley is wearing is the velour tunic used in the first two seasons, not the new double-knit version created for the third. The difference in hue between Spock's tunic and McCoy's can be noticed in certain shots.

In the United Kingdom, the BBC skipped this episode in all runs of the series through to the early 1990s. An official BBC statement by Sheila Cundy of the Programme Correspondence Section reads: "After very careful consideration a top level decision was made not to screen the episodes entitled "Empath" [sic], "Whom The Gods Destroy" [sic], ""Plato's Stepchildren"" and ""Miri"" [actually transmitted in 1970, but not re-aired until the '90s], because they all dealt most unpleasantly with the already unpleasant subjects of madness, torture, sadism and disease" (BBC form letter, undated, Reference 28/SPC). "The Empath" was finally shown for the first time on 5 January1994. It had previously been shown on Sky One, a subscription satellite TV channel. (citation needed • edit)